Contacts of the strand formed by residues 207 - 212 (chain B) in PDB entry 3V3H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B PRO 3.9 4.8 + - - +
141B LEU* 3.5 17.7 - - + +
143B VAL* 3.7 19.5 - - + +
195B PRO* 3.7 3.1 - - - +
196B GLY 2.8 36.9 + - - +
197B SER 3.7 20.6 - - - +
198B LEU* 3.7 9.0 - - + +
205B GLU 3.7 0.2 - - - -
206B CYS* 1.3 92.5 - - - +
208B THR* 1.3 71.5 + - - +
209B TRP* 3.3 35.7 - - + +
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PRO* 3.9 13.5 - - + +
84B LEU* 3.8 30.7 - - + +
88B TYR* 4.8 4.3 + - - -
138B PRO 5.0 4.7 + - - -
139B ASP* 5.0 6.2 - - - +
141B LEU 2.9 13.2 + - - -
142B ALA* 3.4 4.0 - - - +
143B VAL 3.2 21.3 + - - -
193B THR* 3.7 19.3 - - - +
194B TYR 4.0 5.8 - - - +
195B PRO* 4.7 4.0 - - + +
207B VAL* 1.3 72.3 - - - +
209B TRP* 1.3 61.5 + - - +
210B ILE* 3.7 3.4 + - + +
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Residues in contact with TRP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER* 3.0 21.0 + - - -
107B HIS* 3.6 18.6 - + - -
117B GLU* 4.6 0.4 - - - -
119B HIS* 3.5 40.2 - + - -
143B VAL* 3.3 44.4 - - + -
145B GLY* 4.7 3.1 - - - -
192B TRP 4.3 0.2 - - - -
193B THR* 2.8 35.4 + - - -
194B TYR* 2.9 39.5 + + + +
196B GLY* 3.8 10.8 - - - -
197B SER 2.9 29.1 + - - +
198B LEU* 5.2 0.9 - - - -
199B THR* 3.9 15.3 - - + -
207B VAL* 3.3 19.1 - - + +
208B THR* 1.3 71.2 - - - +
210B ILE* 1.3 57.4 + - - +
211B VAL* 4.1 10.1 - - + -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.7 44.6 - - + -
79B LEU* 4.2 19.7 - - + -
83B PRO* 3.9 26.2 - - + -
84B LEU* 4.2 14.8 - - + -
142B ALA* 4.8 1.8 - - + -
143B VAL 3.0 9.6 + - - +
144B LEU* 3.3 13.6 - - + +
145B GLY 2.8 24.3 + - - -
191B TYR* 3.9 21.1 - - + -
192B TRP 3.4 3.6 - - - -
193B THR* 4.2 1.1 - - - +
208B THR* 4.2 7.2 - - + +
209B TRP* 1.3 79.0 - - - +
211B VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.0 19.1 - - + -
107B HIS* 4.0 36.1 - - + +
117B GLU* 5.4 0.7 - - - +
145B GLY* 3.5 12.6 - - - +
147B PHE* 3.6 36.8 - - + -
191B TYR* 3.3 2.0 - - - -
192B TRP* 2.8 41.8 + - + +
194B TYR* 4.8 3.8 - - + -
209B TRP* 4.3 13.2 - - + -
210B ILE* 1.3 76.4 - - - +
212B LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.1 6.5 - - + -
144B LEU* 3.7 25.6 - - + -
145B GLY 2.8 16.5 + - - +
146B ILE* 3.7 17.9 - - + -
147B PHE* 3.8 22.9 + - - -
185B LEU* 5.0 0.7 - - + -
186B PRO* 3.6 33.7 - - + -
188B SER 4.2 1.6 - - - +
189B LEU* 3.8 33.4 - - + +
190B ASP 3.5 13.9 - - - +
191B TYR* 4.0 7.9 - - + -
192B TRP* 3.8 0.7 - - - -
210B ILE 3.9 0.2 + - - -
211B VAL* 1.3 73.1 - - - +
213B LYS* 1.3 64.4 + - - +
214B GLU 3.5 13.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il